ETHZ/Parameters

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== Model Parameters ==
== Model Parameters ==
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! Parameter                       
 +
! Value
 +
! Description
 +
! Comments
 +
!
 +
! Parameter                       
 +
! Value
 +
! Description
 +
! Comments
 +
|-
 +
| c<sub>1</sub><sup>max</sup>
 +
| 0.01 [mM/h]
 +
| max. transcription rate of constitutive promoter (per gene)
 +
| promoter no. J23105; Reference: Estimate
 +
|
 +
| c<sub>2</sub><sup>max</sup>
 +
| 0.01 [mM/h]
 +
| max. transcription rate of luxR-activated promoter (per gene)
 +
| Reference: Estimate
 +
|-
 +
| l<sup>hi</sup>
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| 25
 +
| high-copy plasmid number
 +
| Reference: Estimate
 +
|
 +
| l<sup>lo</sup>
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| 5
 +
| low-copy plasmid number
 +
| Reference: Estimate
 +
|-
 +
| a<sub>Q<sub>2</sub>,R</sub>
 +
| 0.1 - 0.2
 +
| basic production of Q<sub>2</sub>/R-inhibited genes
 +
| Reference: Conclusions after discussion
 +
|
 +
| a<sub>Q<sub>2</sub></sub>
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| 0.1 - 0.2
 +
| basic production of Q<sub>2</sub>-inhibited genes
 +
| Reference: Conclusions after discussion
 +
|-
 +
| a<sub>Q<sub>1</sub>,S</sub>
 +
| 0.1 - 0.2
 +
| basic production of Q<sub>1</sub>/S-inhibited genes
 +
| Reference: Conclusions after discussion
 +
|
 +
| a<sub>Q<sub>1</sub></sub>
 +
| 0.1 - 0.2
 +
| basic production of Q<sub>1</sub>-inhibited genes
 +
| Reference: Conclusions after discussion
 +
|-
 +
| a<sub>Q<sub>2</sub>,S</sub>
 +
| 0.1 - 0.2
 +
| basic production of Q<sub>2</sub>/S-inhibited genes
 +
| Reference: Conclusions after discussion
 +
|
 +
| a<sub>Q<sub>1</sub>,R</sub>
 +
| 0.1 - 0.2
 +
| basic production of Q<sub>1</sub>/R-inhibited genes
 +
| Reference: Conclusions after discussion
 +
|-
 +
| Degradation constants
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
| d<sub>R</sub>
 +
| 2.31e-3 [per sec]
 +
| degradation of lacI
 +
| Ref. [10]
 +
|
 +
| d<sub>S</sub>
 +
| 1e-5 [pro sec]/2.31e-3 [per sec]
 +
| degradation of tetR
 +
| Ref. [9]/ Ref. [10]
 +
|-
 +
| d<sub>L</sub>
 +
| 1e-3 - 1e-4 [per sec]
 +
| degradation of luxR
 +
| Ref: [6]
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|
 +
| d<sub>Q<sub>1</sub></sub>
 +
| 7e-4 [per sec]
 +
| degradation of cI
 +
| Ref. [7]
 +
|-
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| d<sub>Q<sub>2</sub></sub>
 +
|
 +
| degradation of p22cII
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|
 +
|
 +
| d<sub>YFP</sub>
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| 6.3e-3 [per min]
 +
| degradation of YFP
 +
| suppl. mat. to Ref. [8] corresponding to a half life of 110min
 +
|-
 +
| d<sub>GFP</sub>
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| 6.3e-3 [per min]
 +
| degradation of GFP
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| in analogy to YFP
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|
 +
| d<sub>RFP</sub>
 +
| 6.3e-3 [per min]
 +
| degradation of RFP
 +
| in analogy to YFP
 +
|-
 +
| d<sub>CFP</sub>
 +
| 6.3e-3 [per min]
 +
| degradation of CFP
 +
| in analogy to YFP
 +
|
 +
| K<sub>R</sub>
 +
| 0.1 - 1 [pM]
 +
| lacI repressor dissociation constant
 +
| Ref. [2]
 +
|-
 +
| K<sub>I<sub>R</sub></sub>
 +
| 1.3 [&#181;M]
 +
| IPTG-lacI repressor dissociation constant
 +
| Ref. [2]
 +
|
 +
| K<sub>S</sub>
 +
| 179 [pM]
 +
| tetR repressor dissociation constant
 +
| Ref. [1]
 +
|-
 +
| K<sub>I<sub>S</sub></sub>
 +
| 893 [pM]
 +
| aTc-tetR repressor dissociation constant
 +
| Ref. [1]
 +
|
 +
| K<sub>L</sub>
 +
| 55 - 520 [nM]
 +
| luxR activator dissociation constant
 +
| Ref: [6]
 +
|-
 +
| K<sub>I<sub>L</sub></sub>
 +
| 0.09 - 1 [&#181;M]
 +
| AHL-luxR activator dissociation constant
 +
| Ref: [6]
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|
 +
| K<sub>Q<sub>1</sub></sub>
 +
|
 +
* 8 [pM]
 +
* 50 [nM]
 +
| cI repressor dissociation constant
 +
|
 +
* Ref. [12]
 +
* starting with values of Ref. [6] and using Ref. [3]
 +
|-
 +
| K<sub>Q<sub>2</sub></sub>
 +
| 0.577 [&#181;M]
 +
| p22cII repressor dissociation constant
 +
| Ref. [11]. Note that they use a protein cII and we have p22cII. Does that match?
 +
|
 +
| n<sub>R</sub>
 +
| 1
 +
| lacI repressor Hill cooperativity
 +
| Ref. [5]
 +
|-
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| n<sub>I<sub>R</sub></sub>
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| 2
 +
| IPTG-lacI repressor Hill cooperativity
 +
| Ref. [5]
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|
 +
| n<sub>S</sub>
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| 3
 +
| tetR repressor Hill cooperativity
 +
| Ref. [3]
 +
|-
 +
| n<sub>I<sub>S</sub></sub>
 +
| 2 (1.5-2.5)
 +
| aTc-tetR repressor Hill cooperativity
 +
|Ref. [3]
 +
|
 +
| n<sub>L</sub>
 +
| 2
 +
| luxR activator Hill cooperativity
 +
| Ref: [6]
 +
|-
 +
| n<sub>I<sub>L</sub></sub>
 +
| 1
 +
| AHL-luxR activator Hill cooperativity
 +
| Ref. [3]
 +
|
 +
| n<sub>Q<sub>1</sub></sub>
 +
| 2
 +
| cI repressor Hill cooperativity
 +
| Ref. [12]
 +
|-
 +
| n<sub>Q<sub>2</sub></sub>
 +
| 4
 +
| p22cII repressor Hill cooperativity
 +
| Ref. [11]. Note that they use a protein cII and we have p22cII. Does that match?
 +
|-
 +
|}
 +
 +
 +
 +
{| class="wikitable" border="1" cellspacing="0" cellpadding="2" style="text-align:left; margin: 1em 1em 1em 0; background: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;"
 +
! Parameter                       
 +
! Value
 +
! Description
 +
! Comments
 +
!
 +
! Parameter                       
 +
! Value
 +
! Description
 +
! Comments
 +
|-
 +
| c<sub>1</sub><sup>max</sup>
 +
| 0.01 [mM/h]
 +
| max. transcription rate of constitutive promoter (per gene)
 +
| promoter no. J23105; Reference: Estimate
 +
|
 +
| c<sub>1</sub><sup>max</sup>
 +
| 0.01 [mM/h]
 +
| max. transcription rate of constitutive promoter (per gene)
 +
| promoter no. J23105; Reference: Estimate
 +
|-
 +
|}
 +
 +
<br>
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{| class="wikitable" border="1" cellspacing="0" cellpadding="2" style="text-align:left; margin: 1em 1em 1em 0; background: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;"

Revision as of 11:55, 13 October 2007

Introduction

blabla


Model Parameters

Parameter Value Description Comments Parameter Value Description Comments
c1max 0.01 [mM/h] max. transcription rate of constitutive promoter (per gene) promoter no. J23105; Reference: Estimate c2max 0.01 [mM/h] max. transcription rate of luxR-activated promoter (per gene) Reference: Estimate
lhi 25 high-copy plasmid number Reference: Estimate llo 5 low-copy plasmid number Reference: Estimate
aQ2,R 0.1 - 0.2 basic production of Q2/R-inhibited genes Reference: Conclusions after discussion aQ2 0.1 - 0.2 basic production of Q2-inhibited genes Reference: Conclusions after discussion
aQ1,S 0.1 - 0.2 basic production of Q1/S-inhibited genes Reference: Conclusions after discussion aQ1 0.1 - 0.2 basic production of Q1-inhibited genes Reference: Conclusions after discussion
aQ2,S 0.1 - 0.2 basic production of Q2/S-inhibited genes Reference: Conclusions after discussion aQ1,R 0.1 - 0.2 basic production of Q1/R-inhibited genes Reference: Conclusions after discussion
Degradation constants
dR 2.31e-3 [per sec] degradation of lacI Ref. [10] dS 1e-5 [pro sec]/2.31e-3 [per sec] degradation of tetR Ref. [9]/ Ref. [10]
dL 1e-3 - 1e-4 [per sec] degradation of luxR Ref: [6] dQ1 7e-4 [per sec] degradation of cI Ref. [7]
dQ2 degradation of p22cII dYFP 6.3e-3 [per min] degradation of YFP suppl. mat. to Ref. [8] corresponding to a half life of 110min
dGFP 6.3e-3 [per min] degradation of GFP in analogy to YFP dRFP 6.3e-3 [per min] degradation of RFP in analogy to YFP
dCFP 6.3e-3 [per min] degradation of CFP in analogy to YFP KR 0.1 - 1 [pM] lacI repressor dissociation constant Ref. [2]
KIR 1.3 [µM] IPTG-lacI repressor dissociation constant Ref. [2] KS 179 [pM] tetR repressor dissociation constant Ref. [1]
KIS 893 [pM] aTc-tetR repressor dissociation constant Ref. [1] KL 55 - 520 [nM] luxR activator dissociation constant Ref: [6]
KIL 0.09 - 1 [µM] AHL-luxR activator dissociation constant Ref: [6] KQ1
  • 8 [pM]
  • 50 [nM]
cI repressor dissociation constant
  • Ref. [12]
  • starting with values of Ref. [6] and using Ref. [3]
KQ2 0.577 [µM] p22cII repressor dissociation constant Ref. [11]. Note that they use a protein cII and we have p22cII. Does that match? nR 1 lacI repressor Hill cooperativity Ref. [5]
nIR 2 IPTG-lacI repressor Hill cooperativity Ref. [5] nS 3 tetR repressor Hill cooperativity Ref. [3]
nIS 2 (1.5-2.5) aTc-tetR repressor Hill cooperativity Ref. [3] nL 2 luxR activator Hill cooperativity Ref: [6]
nIL 1 AHL-luxR activator Hill cooperativity Ref. [3] nQ1 2 cI repressor Hill cooperativity Ref. [12]
nQ2 4 p22cII repressor Hill cooperativity Ref. [11]. Note that they use a protein cII and we have p22cII. Does that match?


Parameter Value Description Comments Parameter Value Description Comments
c1max 0.01 [mM/h] max. transcription rate of constitutive promoter (per gene) promoter no. J23105; Reference: Estimate c1max 0.01 [mM/h] max. transcription rate of constitutive promoter (per gene) promoter no. J23105; Reference: Estimate


Parameter Value Description Comments
c1max 0.01 [mM/h] max. transcription rate of constitutive promoter (per gene) promoter no. J23105; Reference: Estimate
c2max 0.01 [mM/h] max. transcription rate of luxR-activated promoter (per gene) Reference: Estimate
lhi 25 high-copy plasmid number Reference: Estimate
llo 5 low-copy plasmid number Reference: Estimate
aQ2,R 0.1 - 0.2 basic production of Q2/R-inhibited genes Reference: Conclusions after discussion
aQ2 0.1 - 0.2 basic production of Q2-inhibited genes Reference: Conclusions after discussion
aQ1,S 0.1 - 0.2 basic production of Q1/S-inhibited genes Reference: Conclusions after discussion
aQ1 0.1 - 0.2 basic production of Q1-inhibited genes Reference: Conclusions after discussion
aQ2,S 0.1 - 0.2 basic production of Q2/S-inhibited genes Reference: Conclusions after discussion
aQ1,R 0.1 - 0.2 basic production of Q1/R-inhibited genes Reference: Conclusions after discussion
dR 2.31e-3 [per sec] degradation of lacI Ref. [10]
dS 1e-5 [pro sec]/2.31e-3 [per sec] degradation of tetR Ref. [9]/ Ref. [10]
dL 1e-3 - 1e-4 [per sec] degradation of luxR Ref: [6]
dQ1 7e-4 [per sec] degradation of cI Ref. [7]
dQ2 degradation of p22cII
dYFP 6.3e-3 [per min] degradation of YFP suppl. mat. to Ref. [8] corresponding to a half life of 110min
dGFP 6.3e-3 [per min] degradation of GFP in analogy to YFP
dRFP 6.3e-3 [per min] degradation of RFP in analogy to YFP
dCFP 6.3e-3 [per min] degradation of CFP in analogy to YFP
KR 0.1 - 1 [pM] lacI repressor dissociation constant Ref. [2]
KIR 1.3 [µM] IPTG-lacI repressor dissociation constant Ref. [2]
KS 179 [pM] tetR repressor dissociation constant Ref. [1]
KIS 893 [pM] aTc-tetR repressor dissociation constant Ref. [1]
KL 55 - 520 [nM] luxR activator dissociation constant Ref: [6]
KIL 0.09 - 1 [µM] AHL-luxR activator dissociation constant Ref: [6]
KQ1
  • 8 [pM]
  • 50 [nM]
cI repressor dissociation constant
  • Ref. [12]
  • starting with values of Ref. [6] and using Ref. [3]
KQ2 0.577 [µM] p22cII repressor dissociation constant Ref. [11]. Note that they use a protein cII and we have p22cII. Does that match?
nR 1 lacI repressor Hill cooperativity Ref. [5]
nIR 2 IPTG-lacI repressor Hill cooperativity Ref. [5]
nS 3 tetR repressor Hill cooperativity Ref. [3]
nIS 2 (1.5-2.5) aTc-tetR repressor Hill cooperativity Ref. [3]
nL 2 luxR activator Hill cooperativity Ref: [6]
nIL 1 AHL-luxR activator Hill cooperativity Ref. [3]
nQ1 2 cI repressor Hill cooperativity Ref. [12]
nQ2 4 p22cII repressor Hill cooperativity Ref. [11]. Note that they use a protein cII and we have p22cII. Does that match?

References

[http://www.pnas.org/cgi/content/abstract/104/8/2643 [1] Weber W et al.] "A synthetic time-delay circuit in mammalian cells and mice", P Natl Acad Sci USA 104(8):2643-2648, 2007
[http://www.pnas.org/cgi/content/full/100/13/7702?ck=nck [2] Setty Y et al.] "Detailed map of a cis-regulatory input function", P Natl Acad Sci USA 100(13):7702-7707, 2003
[http://ieeexplore.ieee.org/iel5/9711/30654/01416417.pdf [3] Braun D et al.] "Parameter Estimation for Two Synthetic Gene Networks: A Case Study", ICASSP 5:769-772, 2005
[http://www.nature.com/nature/journal/v435/n7038/suppinfo/nature03508.html [4] Fung E et al.] "A synthetic gene--metabolic oscillator", Nature 435:118-122, 2005 (supplementary material)
[http://dx.doi.org/10.1016/j.jbiotec.2005.08.030 [5] Iadevaia S and Mantzais NV] "Genetic network driven control of PHBV copolymer composition", J Biotechnol 122(1):99-121, 2006
[http://dx.doi.org/10.1016/j.biosystems.2005.04.006 [6] Goryachev AB et al.] "Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants", Biosystems 83(2-3):178-187, 2004
[http://www.genetics.org/cgi/content/abstract/149/4/1633 [7] Arkin A et al.] "Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-Infected Escherichia coli cells", Genetics 149: 1633-1648, 1998
[http://download.cell.com/supplementarydata/cell/107/6/739/DC1/index.htm [8] Colman-Lerner A et al.] "Yeast Cbk1 and Mob2 Activate Daughter-Specific Genetic Programs to Induce Asymmetric Cell Fates", Cell 107(6): 739-750, 2001 (supplementary material)
[http://www.nature.com/nature/journal/v405/n6786/abs/405590a0.html [9] Becskei A and Serrano L] "Engineering stability in gene networks by autoregulation", Nature 405: 590-593, 2000
[http://www.biophysj.org/cgi/content/full/89/6/3873?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&searchid=1&FIRSTINDEX=0&volume=89&firstpage=3873&resourcetype=HWCIT [10] Tuttle et al.] "Model-Driven Designs of an Oscillating Gene Network", Biophys J 89(6):3873-3883, 2005
[http://www.pnas.org/cgi/reprint/99/2/679 [11] McMillen LM et al.] "Synchronizing genetic relaxation oscillators by intercell signaling", P Natl Acad Sci USA 99(2):679-684, 2002
[http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html [12] Basu S et al.] "A synthetic multicellular system for programmed pattern formation", Nature 434:1130-1134, 2005

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